Palise Biochem Exam 3

Define pharmacogenomics and pharmacogenetics. 

1. Pharmacogenomics: This field looks at how all of a person’s genes (the genome) influence their response to medications. It takes a broader, genome-wide approach, focusing on multiple genes and their interactions to understand variations in drug efficacy, safety, and metabolism.

2. Pharmacogenetics: This focuses more narrowly on how variations in a single gene or a small set of genes influence an individual’s response to a specific drug. It’s a subset of pharmacogenomics and is used to predict the best drug or dose based on an individual’s genetic makeup.

Recognize the importance of pharmacogenomics in the osteopathic medicine context.

1. Personalized medicine is one of the variables that must be analyzed, aiming for a safe treatment and the best choice of drug and dose on an individual basis. Personalized medicine is the best choice of drug and dose on an individual basis for a safe treatment. Information on the individual genetic variability in the DNA sequence of drug targets, drug-metabolizing enzymes, or disease genes in RNA expression, or protein translation of genes affecting drug response and drug safety.

List the common genetic polymorphisms related to metabolism and give examples.

1. Phase I: creating functional groups or modifying existing ones (oxidation, reduction, hydrolysis) → mostly activates drugs. 

2. Phase II: conjugation (acid addition) → mostly inactivates drugs. 

3. Pharmacogenomics affecting Phase I metabolism:

   1. CYP2C9: Substrates include Phenytoin and Warfarin. A poor metabolizer (loss-of-function polymorphism) is at risk of toxicity and bleeding while an ultrarapid metabolizer will see a lack of effect.

   2. CYP2C19: Substrates include Omeprazole and Clopidogrel. Consequences in a poor metabolizer include toxicity and a lack of effect, respectively. For an ultrarapid metabolizer (gain-of-function polymorphism), both Omeprazole and Clopidogrel will show a lack of effect.

   3. CYP2D6: Substrates for this enzyme are Codeine, Fluoxetine, Paroxetine, and Nortriptyline. A poor metabolizer with CYP2D6 substrates will have a lack of effect.

   4. CYP3A5: Substrates include Tacrolimus and Vincristine, both of which are not prodrugs. Poor metabolizers have reduced enzyme activity and patients have more adverse effects. An ultrarapid metabolizer with a CYP3A5 substrate has enhanced metabolism and decreased efficacy.

4. Pharmacogenomics affecting Phase II metabolism:

   1. N-acetyltransferase type 2 (NAT2): Substrates for this enzyme include INH, Isoniazid, Pyrazinamide, Procainamide, and Caffeine. Rapid acetylators experience reduced toxicity while slow acetylators are at risk for high toxicity.

   2. Urine diphosphate Glucuronosyl Transferase (UGT): This enzyme acts on the prodrug, Irinotecan. Slow metabolizers, which are present in 70% of the population, experience higher toxicity.

   3. Thiopurine MethylTransferase (TPMT): The sources state that FDA requires genetic tests before starting treatment for TPMT genotype (e.g., patients who require azathioprine therapy) are now routinely tested for the TPMT genotype.

   4. Pseudocholinesterase (BuACHE): This enzyme acts on the substrate, Succinylcholine. High enzymatic activity results in respiratory paralysis and malignant hyperthermia. Low enzymatic activity results in respiratory paralysis.

Recognize clinically relevant genetic polymorphisms in pharmacodynamic settings.

1. Polymorphism in VKORC1: Results in lower protein expression and increased Warfarin sensitivity. The management is to lower the drug dose.

2. B2-adrenergic receptor: A variant in a specific amino acid leads to a higher downregulation than in a wild-type individual. In this case, the effect of the drug (at a therapeutic dose) is reduced. Management increases the dosage.

3. CYP polymorphism means that metabolization is affected, but the distribution is less likely to be affected.

Discuss the consequences and management of clinically relevant polymorphisms.

1. Polymorphism in Vit Reductase (VKOR):

   1. Higher expression → decreases Warfarin’s effect → increase dose.

   2. Lower expression → more Warfarin’s effect → lower dose. 

2. B2-adrenergic receptor:

   1. Resistance to down-regulation → high effect of drug that acts as agonist → overstimulation of B2-receptor → toxicity → reduce dose.

   2. Higher down-regulation → effect of drug is reduced → lack of drug effect → increase dose. 

      Know toxicology-related terms and the branches of toxicology.

      1. Toxicant - any toxic chemical / agent.

      2. Poison - a substance that through its chemical action kills, injures, or impairs an organism.

      3. Xenobiotic agent - any substance foreign to the body.

      4. Hazard -  innate toxic effect of a chemical (hazards pose risks only if the exposure is sufficiently high).

      5. Threshold -  the dose below which no effect occurs.

      6. Toxic Effect - abnormal, harmful, or undesirable effects that cause anatomical or functional damage, irreversible physical changes, or increases the susceptibility to other biological, chemical, or environmental stresses.

      7. Carcinogen - a substance that can cause cancer.

      8. Mutagen - a substance that can cause genetic mutations.

      9. Teratogen - a substance that can cause physical defects in the developing embryo.

      10. Branches of Toxicology:

          1. Clinical Toxicology - Study of the toxic effects of various drugs in living organisms, the methods of detection, diagnosis, and treatment.

          2. Developmental Toxicology - Study of adverse effects of various toxicants on developing organisms anytime during their lifespan.

          3. Environmental Toxicology - Study of the adverse effects of various environmental toxic substances, pollutants on organisms, populations, ecosystems, and the biosphere.

          4. Forensic Toxicology -  medical evidence of poisoning to establish the extent to which poisons were involved in human deaths.

          5. Mechanistic Toxicology -  identification and understanding cellular, biochemical and molecular basis by which chemicals exert toxic effects.

          6. Regulatory Toxicology -  scientific knowledge to develop regulations and other strategies for reducing and controlling exposures to dangerous chemicals.

          7. Economic Toxicology - Related to Food and Drug toxicology.

          8. Industrial Toxicology -  study of the nature and types of chemical substances emitted by the industries and ambient air and water.

          9. Genetic Toxicology -  study of deleterious effects of xenobiotics on the genetic constitution of individuals. 

   
   
   

   2. Describe sources/exposures and types of poisoning.

   
   

   3. Understand the importance of dose, dose-response curves, and that only the dose distinguishes a remedy from a poison.

      1. Dose: A dose refers to the amount of a substance administered or absorbed by an organism. It's typically measured in milligrams (mg) or grams (g).

      2. Dose-Response Curves: These graphical representations illustrate the relationship between the dose of a substance and the magnitude of its effect. They also establish chemical effects, determine threshold effects, and determine the rate at which the effect occurs. 

   They are essential tools in toxicology for:

   1. Estimating risk.

   2. Determining safe exposure levels.

   3. Understanding the potential for harm.

   
   

   4. Describe the clinical aspects of treatment of acute poisonings.

      1. Before arrival at treatment center:

         1. Obtain useful information, induce emesis, decontamination, adsorbents (charcoal) can bind to poison in GI to reduce absorption into the bloodstream, rapid transport to ER. 

      2. At treatment center:

         1. Perform initial exam, remove unabsorbed toxicant using emesis unless it contradicts, administer specific antidotes, give supportive treatment, speed up the elimination of absorbed toxicant. 

   
   

   5. Describe factors involved in the extent of cell or tissue damage from a toxicant.

      1. Dose and nature of exposure (acute vs intermittent vs chronic).

      2. Tissue/cell characteristics (protective mechanisms, regenerative capacity).

      3. Rate at which initial insult occurs.

      4. Progression factors (inflammation).

   
   

   6. Recognize the major mechanisms of toxicity.

      1. Receptor-ligand interactions (PCBs and dioxin).

      2. Interference with E production.

      3. Covalent binding to biomolecules:

         1. Proteins - alter structure and function.

         2. Lipids - disrupt CM.

         3. Nucleic acids - mutations.

      4. Oxidative stress (generation of ROS).

      5. Perturbation of calcium homeostasis.

      6. Selective cell death.

      7. Dysregulation of gene expression.

      8. Cell death signaling (necrosis; apoptosis).

   
   
   
   

   7. Basics on types of Poisons/toxic exposures and their effects: Drug, Metals, Dioxins, natural chemical (mushroom), pollutants (tobacco smoke, carbon monoxide, particulate matter). 

      1. Drugs:

         1. Source: Prescription medications, over-the-counter drugs, illicit drugs

         2. Effects: Wide-ranging, depending on the drug and the dose. Can include:

            1. Therapeutic effects: Intended beneficial effects.

            2. Toxic effects: Unintended harmful effects, such as allergic reactions, organ damage, or even death.

      2. Metals:

         1. Source: Environmental exposure (water, soil, air), occupational exposure, contaminated food, some consumer products.

         2. Effects: Vary greatly depending on the specific metal and the dose. 

            1. Neurotoxicity: Damage to the nervous system.

            2. Nephrotoxicity: Damage to the kidneys.

            3. Hepatotoxicity: Damage to the liver.

            4. Carcinogenesis: Increased risk of cancer.

            5. Teratogenesis: Birth defects.

      3. Dioxins:

         1. Source: Industrial byproducts, natural sources (forest fires, volcanic eruptions).

         2. Effects: Highly toxic, persistent environmental pollutants. Can cause:

            1. Teratogenesis: Birth defects.

            2. Cancer: Increased risk of various cancers.

            3. Immunosuppression: Weakening of the immune system.

            4. Endocrine disruption: Interference with hormone function.

            5. Liver damage

            6. Chloracne: Skin lesions.

      4. Natural Chemicals (Mushrooms):

         1. Source: Certain species of wild mushrooms, particularly Amanita phalloides (death cap).

         2. Effects: Can contain cyclic peptide hepatotoxins that cause:

            1. Hepatorenal Syndrome: Severe damage to the liver and kidneys.

            2. Death: Can be fatal if not treated promptly.

      5. Pollutants:

         1. Source: Various environmental sources:

            1. Tobacco Smoke: Contains a complex mixture of thousands of harmful chemicals.

            2. Carbon Monoxide (CO): Produced by incomplete combustion of organic fuels.

            3. Particulate Matter (PM): Mixture of solid and liquid particles suspended in the air.

         2. Effects:

            1. Tobacco Smoke:

               1. COPD, lung cancer, asthma, heart disease, increased risk of various types of cancer, reproductive problems.

            2. Carbon Monoxide (CO):

               1. Binds to hemoglobin, preventing the transport of oxygen to tissues.

            3. Particulate Matter (PM):

               1. Heart disease, stroke, asthma, COPD, lung cancer, respiratory infections.

               2. Other Effects: Diabetes, obesity, cognitive impairment, neurodegenerative diseases.

                  List endogenous accumulations and recognize the functional deficits that can lead to them.

                  1. Endogenous accumulations are generated by the cell itself. They can be harmful or harmless and include accumulations of normal cell constituents (e.g., water, lipids, protein, carbohydrates) and abnormal constituents (e.g., defective proteins, abnormal metabolites, oxidation products, minerals, pigments, fibers, inclusions). Functional deficits can arise from inadequate removal, failed degradation, defects in pathways normally used for removal, and exposure to things with no other means of elimination.

               
               

               2. Name the different types and conditions involving lipid accumulations. 

                  1. Lipid accumulations involve the accumulation of all major classes of lipids: triglycerides (Tgs), cholesterol, cholesterol esters, and phospholipids.

                     1. Foam Cells - cholesterol filled macrophages.

                        1. Atheromas - aggregates of foam cells.

                        2. Xanthomas - clusters of foam cells in the subepithelial connective tissue of the skin and tendons in patients with hyperlipidemia.

                        3. Cholesterolosis - foam cell accumulation in the lamina propria of the gallbladder.

                     2. Cholesterol clefts -  ruptured atheroma → lipids released in extracellular space.

                     3. Niemann-Pick Disease - lysosomal storage disease → accumulation of cholesterol in the body. 

               
               

               3. Name the different conditions and biochemical alterations that can lead to hepatic steatosis (fatty liver).

                  1. Hepatic steatosis is a condition characterized by excessive fat accumulation in the liver. This can occur due to:

                     1. Too much free fat coming into the liver.

                     2. Too much fatty acid synthesis occurs inside the liver.

                     3. Impaired B-oxidation by the liver.

                     4. Excess esterification of fatty acids to triglycerides by the liver.

                     5. Too little apoprotein synthesis by the liver.

                     6. Failure of lipoprotein secretion from the liver. 

               4. Describe and define alcoholic hyaline, Russel bodies, and protein reabsorption droplets.

                  1. Alcoholic Hyaline: This refers to Mallory-Denk bodies, which are eosinophilic (pink-staining) cytoplasmic inclusions found in liver cells, especially in individuals with alcoholic liver disease. 

                  2. Russell Bodies: Russell bodies occur when plasma cells produce excess antibodies, which remain trapped in the endoplasmic reticulum → distended RER.

                  3. Protein Reabsorption Droplets: These are accumulations of proteins when there is excessive protein filtration, as in conditions like nephrotic syndrome. The tubular cells attempt to reabsorb the protein, leading to the formation of these droplets, which appear as eosinophilic inclusions under a microscope.

               
               

               5. Recognize the descriptive categories of exogenous accumulations.

                  1. Substances accumulate because we don’t have anything in our bodies to degrade them. Examples:

                     1. Fibers or dust.

                     2. Metals and minerals.

                     3. Certain microbes.

                     4. Pigments (melanin, tattoo ink, bilirubin, etc). 

               
               

               6. Describe the pathologies associated with the accumulation of hemosiderin and bilirubin and their breakdown products.

                  1. Hemosiderin is an iron-storage complex that accumulates in tissues when there is excess iron.

                  2. Pathologies:

                     1. RBC’s repeatedly broken down → Hemosiderin accumulates in macrophages → Hemorrhage.

                     2. May deposit in reticuloendothelial cells of the liver, spleen, bone marrow.

                  3. Bilirubin is a yellow pigment that results from the breakdown of hemoglobin from red blood cells.

                  4. Pathologies:

                     1. Jaundice: This is the yellowing of the skin and eyes due to excess bilirubin in the blood.

                     2. Hemolytic Anemia: When red blood cells break down rapidly, excess bilirubin is produced, which can overwhelm the liver’s ability to process it.

               
               

               7. Link the histochemical stains and associated colors with the substances detected.

               
               

               8. List, define, and distinguish among the different pigment, mineral, and metal accumulations.

                  1. Pigments: Pigments are colored substances that can accumulate in cells and tissues. They can be endogenous (produced by the body) or exogenous (from outside the body).

                     1. Endogenous Pigments: 

                        1. Melanin: abnormal melanin deposition on gums, melanosis.

                        2. Lipofuscin: vitamin E deficiency, golden-brown deposits, product of oxidative damage.

                        3. Hemosiderin: iron overload, see above. 

                        4. Bilirubin: jaundice, see above.

                     2. Exogenous Pigments: 

                        1. Anthracosis:pneumoconiosis: C-deposits eaten by macrophages.

                        2. Silicosis: inhalation of crystalline silica dust, most common form.

                        3. Talcosis: reaction to chronic inhalation of talc.

                        4. Asbestosis: chronic inhalation of asbestos fibers → interstitial fibrosis.

                        5. Tattoo ink: pigments injected into the dermis → eaten by dermal macrophages → remain undigested.

                        6. Carotenodermia: high b-carotene levels in blood, seen in vegetarians. 

                  2. Minerals: Minerals are inorganic substances that can accumulate in cells and tissues.

                     1. Calcium → Dystrophic or Metastatic Calcification.

                        1. General Mechanism: cell damage → unrestricted entry of Ca into cells → membrane pump damage → can’t pump Ca out of cells → Ca accumulates and binds to free PO4 → crystal formation. 

                        2. Dystrophic Calcification:

                           1. Occurs in areas of necrosis and is NOT associated with hypercalcemia.

                        3. Metastatic Calcification: 

                           1. Occurs in healthy tissues and IS associated with hypercalcemia. 

                  3. Metals: Metals are inorganic elements that can accumulate in cells and tissues.

                     1. Silver: argyria.

                     2. Iron: overload → Hemosiderin.

                     3. Arsenic: blackfoot disease

                     4. Lead: plumbism.

                     5. Bismuth: blackening of tongue.

               
               

               9. Recognize carotenodermia caused by carotenemia.

                  1. Carotenodermia caused by carotenemia is a condition where the skin takes on a yellow-orange tint due to elevated levels of carotenoids in the blood. This happens when someone consumes an excess of carotenoid-rich foods, like carrots, sweet potatoes, or other orange and green vegetables.

               
               

               10. Compare and contrast melanin, lipofuscin, hemosiderin and bilirubin.

               ***Key Comparisons:****

               • Melanin and lipofuscin are primarily found as protective (melanin) or age-related pigments (lipofuscin), while hemosiderin and bilirubin are related to RBC breakdown.

               • Hemosiderin and bilirubin are both derived from hemoglobin degradation, but bilirubin is a key component in bile production, whereas hemosiderin functions as an iron storage complex.

               • Lipofuscin accumulates due to cell damage from aging, whereas melanin accumulates as a protective measure against UV damage.

               
               

               11. Describe the morphology and pathogenesis of hemosiderin-based accumulations.

                   1. Morphology:

                      1. Appearance: golden brown granular deposits, staining blue with Prussian blue stain.

                      2. Location: Found in organs like the liver, lungs, and skin, often within macrophages.

                   2. Pathogenesis:

                      1. Hemolysis releases iron, leading to hemosiderin accumulation in macrophages.

                      2. Hemochromatosis (genetic) or repeated blood transfusions result in iron buildup in organs (liver, heart, pancreas).

               
               

               12. Discuss intracellular inclusions.

                   1. Intracellular inclusions are abnormal structures or substances found within the cells. Inclusions may be endogenous (produced by the cell) or exogenous (introduced from outside, such as viruses or toxins).

                      1. Lewy Bodies (Parkinson disease) - neuronal inclusion of alpha-syneculin.

                      2. Viral Inclusion Bodies - large intranuclear inclusions (herpes), cytoplasmic/negri bodies (rabies). 

               
               
               

               13. Use clinical- and laboratory information to identify and distinguish dystrophic- and metastatic calcification. 

                   1.